import metaphlan3 output to Phyloseq

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3.4 years ago

serene.s • 0

Hi I wanted to import the metaphlan3 results to phyloseq. What I did was that I have extracted only the species names as taxa and their abundances are in %. I made the .txt file to an excel file and it looks like this in the image that I am uploading below. But when I tried to make the otu_table in phyloseq it says that the abundances must numeric. How Do I convert the percentage into numbers? Please help anyone.

Thanks Saraswati enter image description here

Phyloseq metagenomics MetaPhaln3 Genomics • 1.2k views

ADD COMMENT • link updated 3.4 years ago by antonioggsousa 3.2k • written 3.4 years ago by serene.s • 0

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Hi,

Unless that you have at least the total number of reads or fragments per sample, you can't convert from percentage to absolute counts. Even if you have the total number of reads/fragments per sample, the percentages were probably rounded, meaning that you really can't get the original absolute counts in that case.

I hope that clarifies your question,

António

ADD REPLY • link 3.4 years ago by antonioggsousa 3.2k

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